Dear FreeSurfer Experts,

I write in regard to the posting on calculating GM measures on a lobar basis.

I had a couple of quick questions:

1) Having derived a lobesfile using mri_annotation2label --subject <name> --hemi lh --lobesStrict lobesfile

one uses

mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.lobesfile.stats -b -a ../label/lh.lobesfile.annot subject lh white

a) Why is the -cortex ../label/lh.cortex.label option needed ? I thought this is needed if one wants to pass cortical label for computing statisitcs across all of the cortex ?

When I repeat the command without it the stats at the bottom of the lobar stats file are the same. However the total number of vertices and white surface area total at the top of the stats file are different and without the -cortex option the average thickness at the top disappears - why is this ?

Should the cortex flag be included or not for lobar GM volumes

b) Does the flag white refer to areas based on white matter in which case if one wants areas based on pial surface should pial flag be used ?

2) What would the approach be to get lobar measures as above but for white matter instead ?

Thanks.

Mahinda